There can be two reasons:
(1) You are using matrox's mga module. They have
'program chip core to production level frequency
instead of bios safe one' in their changelog.
Although difference 100% makes (2) more probably.
(2) matroxfb does not try to activate any AGP transfer
mode. Maybe some X driver tries and succeeds.
You can try:
time dd if=/dev/zero of=/dev/fb0 bs=1M count=8
before X and after X. If times are same, then it is
chip core frequency. If times are 2:1, it is either
chip memory freqency, or AGP...
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